high performance computing on graphics processing units: hgpu.org

Applications

hgpu.org » Applications » Chemistry

Efficient Parallelization of the Stochastic Simulation Algorithm for Chemically Reacting Systems On the Graphics Processing Unit

Hong Li, Linda Petzold

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Tags: Biology, Chemistry, CUDA, nVidia, nVidia GeForce 8800 GTX, Stochastic simulation

May 10, 2011 by hgpu

Improving numerical reproducibility and stability in large-scale numerical simulations on GPUs

Michela Taufer, Omar Padron, Philip Saponaro, Sandeep Patel

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Tags: Chemistry, CUDA, Floating point error, Molecular dynamics, nVidia, Tesla S1070

April 25, 2011 by hgpu

GPU-Based Implementations of the Noniterative Regularized-CCSD(T) Corrections: Applications to Strongly Correlated Systems

Wenjing Ma, Sriram Krishnamoorthy, Oreste Villa, Karol Kowalski

Tags: Chemistry, Molecular modeling

April 15, 2011 by hgpu

GPGPU supported cooperative acceleration in molecular dynamics

Gang Chen, Guobo Li, Songwen Pei, Baifeng Wu

Tags: ATI, Brook, Chemistry, Molecular dynamics

April 5, 2011 by hgpu

Accelerating Molecular Docking Calculations Using Graphics Processing Units

Oliver Korb, Thomas Stutzle, Thomas E. Exner

Tags: Algorithms, Chemistry, Molecular modeling

March 28, 2011 by hgpu

GPU Acceleration of High-Speed Collision Molecular Dynamics Simulation

Canqun Yang, Qiang Wu, Juan Chen, Zhen Ge

Tags: Chemistry, CUDA, Molecular dynamics, nVidia, Tesla C870

March 25, 2011 by hgpu

Evaluating force field accuracy with long-time simulations of a beta-hairpin tryptophan zipper peptide

N. R. Hayre, R. R. Singh, D. L. Cox

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Tags: Biophysics, Chemistry, CUDA, Molecular dynamics, nVidia, nVidia GeForce GTX 285

March 22, 2011 by hgpu

GPU based acceleration of first principles calculation

H. Tomono, M. Aoki, T. Iitaka, K. Tsumuraya

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Tags: Chemistry, CUDA, FFT, Molecular modeling, nVidia, nVidia GeForce GTX 285

March 16, 2011 by hgpu

Automatic Generation of Multicore Chemical Kernels

John C. Linford, John Michalakes, Manish Vachharajani, Adrian Sandu

Tags: Cell processor, Chemistry, Code generation, Computer science, CUDA, nVidia, OpenMP

March 6, 2011 by hgpu

Redesigning combustion modeling algorithms for the Graphics Processing Unit (GPU): Chemical kinetic rate evaluation and ordinary differential equation integration

Yu Shi, William H. Green, Hsi-Wu Wong, Oluwayemisi O. Oluwole

Tags: Chemistry, Computational modelling, CUDA, nVidia, nVidia GeForce GTX 260, Tesla C2050

March 4, 2011 by hgpu

Performance of inverse atomistic scale fracture modeling on GPGPU architectures

A.P. Iliopoulos, J.G. Michopoulos, S.G. Lambrakos, N. Bernstein

Tags: Chemistry, Molecular dynamics, Performance

March 1, 2011 by hgpu

Accelerating Molecular Dynamics Simulations with GPUs

John Paul Walters, Vidyananth Balu, Vipin Chaudhary, David Kofke, Andrew Schultz

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Tags: Chemistry, CUDA, Molecular dynamics, Molecular simulation, nVidia, nVidia GeForce 8800 GTX

February 28, 2011 by hgpu

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Octo-Tiger: Astrophysics program simulating the evolution of star systems based on the fast multipole method on adaptive Octrees

Stellar Mergers with HPX-Kokkos and SYCL: Methods of using an Asynchronous Many-Task Runtime System with SYCL

BAT: A standardized benchmark suite for auto-tuners

Towards a Benchmarking Suite for Kernel Tuners

BenchDirect: A Directed Language Model for Compiler Benchmarks

A Deep Learning Model for Loop Interchange

Bridging Control-Centric and Data-Centric Optimization

Advanced evolutionary computation library built directly on top of PyTorch, created at NNAISENSE

EvoTorch: Scalable Evolutionary Computation in Python

See all packages

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high performance computing on graphics processing units: hgpu.org

Applications

Efficient Parallelization of the Stochastic Simulation Algorithm for Chemically Reacting Systems On the Graphics Processing Unit

Improving numerical reproducibility and stability in large-scale numerical simulations on GPUs

GPU-Based Implementations of the Noniterative Regularized-CCSD(T) Corrections: Applications to Strongly Correlated Systems

GPGPU supported cooperative acceleration in molecular dynamics

Accelerating Molecular Docking Calculations Using Graphics Processing Units

GPU Acceleration of High-Speed Collision Molecular Dynamics Simulation

Evaluating force field accuracy with long-time simulations of a beta-hairpin tryptophan zipper peptide

GPU based acceleration of first principles calculation

Automatic Generation of Multicore Chemical Kernels

Redesigning combustion modeling algorithms for the Graphics Processing Unit (GPU): Chemical kinetic rate evaluation and ordinary differential equation integration

Performance of inverse atomistic scale fracture modeling on GPGPU architectures

Accelerating Molecular Dynamics Simulations with GPUs

Recent source codes

E2C-Sim: a simulator and workload generator for Edge-to-Cloud environments

Kernel Tuner

Clava: C/C++ Source-to-Source Tool based on Clang

gpuLik

Octo-Tiger: Astrophysics program simulating the evolution of star systems based on the fast multipole method on adaptive Octrees

BAT: A standardized benchmark suite for auto-tuners

BenchDirect: A Directed Language Model for Compiler Benchmarks

A Deep Learning Model for Loop Interchange

Bridging Control-Centric and Data-Centric Optimization

Advanced evolutionary computation library built directly on top of PyTorch, created at NNAISENSE

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